ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctcatttccggtgtacaacacaagaacaacatcatcaacttaaaatgctgtgtgaaatctgcaataaggacttcataagttcactctatggacatcaaatcttcatactgaatagatgtatcaaattttcttttattgcag

Basic information

species	Zea mays
transcript	GRMZM2G032049_T01
intron #	17
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G032049_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 5'ss of exon 17

GTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctcatttccggtgtacaacacaagaacaacatcatcaacttaaaatgctgtg--tgaaatctgcaataaggacttcataagttca----ctctatggacatcaa--atcttcatactgaat-agatgtatcaaattttcttttattgcag
|| ||||||||||||||||| || | ||||||  ||||||||||||| |||||||||||||||||| |||     |||||||| ||| |||| |||||  || ||||   |  | ||  | | | ||| || |      | | |  ||||| ||  | || |     || |     |  || | |||    |||| || |||  |   | ||||||| ||||| | ||||   | |                
GTTGTAATAACTAACTTGGAGGATGAAAAAGTCATAGACCTTGATGGAAAAATGTGGCCTGATGCTCCTGCAGACGATGCTTCATCCTACTACAAGgtgtctatcatactcactatatgatatacgaaaaata------aatgatgatgctatggatcaacttgcttatgaaacaattgtaggctcattgtctctctgaacacaatttaccttcatattgaattacatgttctacag---------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|194716949|gb|FK934108.1|FK934108

EST:     GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG                         GTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG
genomic: GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctca ... tttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG

EST: gi|211208862|gb|FL472063.1|FL472063

EST:     CAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG                         GTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG
genomic: CAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctca ... tttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG

EST: gi|211147648|gb|FL303726.1|FL303726

EST:     GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG                         GTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG
genomic: GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctca ... tttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG

EST: gi|149100564|gb|EE186649.2|EE186649

EST:     GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAG                         GTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG
genomic: GCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctca ... tttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTGGTAATAACTAACTTGGAAGAAGGAAAAGTACTAGACCTTGATGGCAAAATGTGGCCTGATGCTTCTGATACTGATGCTTCCTCCCACTATAAGgtacctctca ... tttattgcagGTTCCGTTCTCAAGAACTGTCTACATTGAGAAAACTGATTTTCGCCTAAAGGACTCAAAAGACTACTATGGGCTAGCCCCTGGTAAATCTGTCATGCTAA

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 119

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253